Is DOCK6 p.Asn1653= (c.4959C>T) pathogenic?

DOCK6 p.Asn1653= (c.4959C>T) is classified Benign in DOCK6 (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-02-03). Common (popmax 60.3%, mid) — too common for a highly-penetrant pathogenic allele; Associated with Adams-Oliver syndrome 2.

What condition is associated with DOCK6 p.Asn1653= (c.4959C>T)?

DOCK6 p.Asn1653= (c.4959C>T) is associated with Adams-Oliver syndrome 2 (ClinVar).

DOCK6 p.Asn1653=

Q: How common is DOCK6 p.Asn1653= (c.4959C>T) in the general population?

DOCK6 p.Asn1653= (c.4959C>T) is common (popmax 60.3%, mid) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.4959C>T · rs8409 · VCV518283

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Common

common (popmax 60.3%, mid) — too common for a highly-penetrant pathogenic allele

Conditions

Adams-Oliver syndrome 2

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>C here scores Δ0.24 · evaluated, not missing
Constraint at this position
Conservation	phyloP -9.7	GERP -4.3
Overall
CADD	2.034	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 60.3% Middle Eastern · 3,650/6,058 alleles

Filtering AF 58.6% ClinGen BA1/BS1 input FAF95, joint · FAF99 58%

Overall 55.6% 896,027/1,612,608 alleles · common

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	65.9%	2
Middle Easterngrpmax	60.3%	2
European (non-Finnish)	58%	2
Remaining individualsnot grpmax-eligible	54.4%	2
Admixed American	53.8%	2
Finnishnot grpmax-eligible	52%	2
South Asian	49.5%	2
East Asian	46.7%	2
Amishnot grpmax-eligible	39.3%	3
African / African-American	30.7%	3

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: DOCK6
Protein: p.Asn1653=
Coding: c.4959C>T
MANE Select: NM_020812
dbSNP: rs8409
Type: single nucleotide variant
Location: chr19:11208815 (GRCh38)
Gene constraint: LOEUF 0.87 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.78 · 7 PDB
Residue 1653: the docker domain

Full DOCK6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Adams-Oliver syndrome 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DOCK6 p.Asn1653Ser Uncertain significance ★ ⚠ same residue
DOCK6 c.5939+2T>C Pathogenic ★★ same condition
DOCK6 c.807-1G>A Likely pathogenic ★★ same condition
DOCK6 p.Arg1526Ter Pathogenic/Likely pathogenic ★★ same condition
DOCK6 p.Arg184Ter Pathogenic/Likely pathogenic ★★ same condition
DOCK6 p.Arg488Ter Pathogenic/Likely pathogenic ★★ same condition
DOCK6 p.Gln1188Ter Pathogenic/Likely pathogenic ★★ same condition
DOCK6 p.Tyr129Ter Pathogenic/Likely pathogenic ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/dock6-p-asn1653 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown